How to generate a multi fasta file from bam or vcf files for phylogenic analysis like BratNextGen or Gubbins

Question

[fuguchan]

Hi, Biostars

I want to do phelogenic analysis using Gubbins or BratNextGen in bacterial whole genomes. I am planning to analysis about 50 to 70 isolates of bacterial isolates with 2.5M genome size. I would like to know how to create alignment multi fasta file including all of the isolates. To generate Gubbins, I want to discard the locus with low coverage in BWA mapping.

In addition, I have to prepare alignment multi fasta file not using "N" but "-" for unclear basement.

How can I do that?